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Genetic and Epigenetic Control of Disease Occurrence
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Genetic and Epigenetic Control of Disease Occurrence

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (31 October 2023) | Viewed by 18801

Special Issue Editor

Dr. Valentina Gatta

E-Mail Website
Guest Editor
1. Department of Psychological, Health and Territorial Sciences, University of Chieti-Pescara, 66100 Chieti, Italy
2. Center for Advanced Studies and Technology-CAST, University of Chieti-Pescara, 66100 Chieti, Italy
Interests: gene expression profiles; epigenetics; reproduction; medical genetics; gene mutations; gene–environment interactions in human health

Special Issue Information

Dear Colleagues,

The genetic background is an important contributor to susceptibility to human disease. Deciphering the genetic and molecular basis of human traits and disease is a primary problem in biology and personalized medicine. However, an increasing subclass of disease-causing mutations includes changes in the epigenome or in the amount and activity of proteins that can regulate the chromatin structure. Without changing the genomic sequence, epigenetic modifications, in response to a specific environment, could cause genomic susceptibilities, impacting the later development of human diseases.  This Special Issue on “Genetic and Epigenetic Control of Disease Occurrence” aims to highlight recent advances in the field of genomics and transcriptomics towards the translation of genotype to phenotype and the development of analytical methods to understand how the environment and genetics interact to impact health through epigenetics mechanisms. I would like to invite authors to contribute to the collection of manuscripts and review articles on recent advances regarding the molecular basis of human disease. Reports pertaining to potentially damaging isolated variants without strong arguments implicating them as causal defects will be given low priority.

Dr. Valentina Gatta
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetics
  • epigenetics
  • molecular basis
  • personalized medicine
  • complex traits
  • transgenerational inheritance
  • mendelian inheritance

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Published Papers (5 papers)

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Research

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17 pages, 2194 KiB  
Article
DNA Sequence Variations Affecting Serotonin Transporter Transcriptional Regulation and Activity: Do They Impact Alcohol Addiction?
by Giampiero Ferraguti, Silvia Francati, Claudia Codazzo, Giovanna Blaconà, Giancarlo Testino, Antonio Angeloni, Marco Fiore, Mauro Ceccanti and Marco Lucarelli
Int. J. Mol. Sci. 2024, 25(15), 8089; https://doi.org/10.3390/ijms25158089 - 25 Jul 2024
Cited by 2 | Viewed by 1585
Abstract
Genetic features of alcohol dependence have been extensively investigated in recent years. A large body of studies has underlined the important role of genetic variants not only in metabolic pathways but also in the neurobiology of alcohol dependence, mediated by the neuronal circuits [...] Read more.
Genetic features of alcohol dependence have been extensively investigated in recent years. A large body of studies has underlined the important role of genetic variants not only in metabolic pathways but also in the neurobiology of alcohol dependence, mediated by the neuronal circuits regulating reward and craving. Serotonin transporter (5-HTT), encoded by the SLC6A4 gene (Solute carrier family 6-neurotransmitter transporter-member 4), is targeted by antidepressant drugs such as selective serotonin reuptake inhibitors (SSRIs) and plays a pivotal role in serotoninergic transmission; it has been associated with psychiatric diseases and alcohol dependence. Transcriptional regulation and expression of 5-HTT depend not only on epigenetic modifications, among which DNA methylation (CpG and non-CpG) is primarily involved, but also on sequence variations occurring in intron/exon regions and in untranslated regions in 5′ and 3′, being the first sequences important for the splicing machinery and the last for the binding of transcription factors and micro RNAs. This work intends to shed light on the role of sequence variations known to affect the expression or function of 5-HTT in alcohol-dependent individuals. We found a statistically significant difference in the allelic (p = 0.0083) and genotypic (p = 0.0151) frequencies of the tri-allelic polymorphism, with higher function alleles and genotypes more represented in the control population. Furthermore, we identified three haplotypes more frequent in subjects with AUD (p < 0.0001) and one more frequent in the control population (p < 0.0001). The results obtained for the tri-allelic polymorphism in alcohol dependence confirm what is already present in part of the literature. The role of haplotypes requires further studies to be clarified. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Control of Disease Occurrence)
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9 pages, 542 KiB  
Article
Association between Downstream Taste Signaling Genes, Oral Microbiome, and Severe Early Childhood Caries
by Vivianne Cruz de Jesus, Betty-Anne Mittermuller, Pingzhao Hu, Robert J. Schroth and Prashen Chelikani
Int. J. Mol. Sci. 2023, 24(1), 81; https://doi.org/10.3390/ijms24010081 - 21 Dec 2022
Cited by 3 | Viewed by 1973
Abstract
Polymorphisms in taste receptor genes have been shown to play a role in early childhood caries (ECC), a multifactorial, biofilm-mediated disease. This study aimed to evaluate associations between severe-ECC (S-ECC), the oral microbiome, and variants in genes that encode components of the G [...] Read more.
Polymorphisms in taste receptor genes have been shown to play a role in early childhood caries (ECC), a multifactorial, biofilm-mediated disease. This study aimed to evaluate associations between severe-ECC (S-ECC), the oral microbiome, and variants in genes that encode components of the G protein-coupled receptor (GPCR) signaling cascade involved in taste sensation. A total of 176 children (88 caries-free; 88 with S-ECC) were recruited. Analyses of 16S and ITS1 rRNA microbial genes and seven (GNAQ, GNAS, GNAT3, GNAI2, RAC1, RALB, and PLCB2) human genes were pursued using next-generation sequencing. Regression analyses were performed to evaluate associations between genetic variants, S-ECC, and the supragingival plaque microbiome. Results suggest that PLCB2 rs2305645 (T), rs1869901 (G), and rs2305649 (G) alleles had a protective effect on S-ECC (rs2305645, odds ratio (OR) = 0.27 (95% confidence interval (CI): 0.14–0.51); rs1869901, OR = 0.34 (95% CI: 0.20–0.58); and rs2305649, OR = 0.43 (95% CI: 0.26–0.71)). Variants in GNAQ, GNAS, GNAT3, PLCB2, RALB, and RAC1 were associated with oral fungal and bacterial community composition. This study revealed that three loci at PLCB2 are significantly associated with S-ECC. Variants in multiple genes were associated with the composition of dental biofilm. These findings contribute to the current knowledge about the role of genetics in S-ECC. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Control of Disease Occurrence)
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20 pages, 4120 KiB  
Article
Gene Expression and DNA Methylation in Human Papillomavirus Positive and Negative Head and Neck Squamous Cell Carcinomas
by Snežana Hinić, April Rich, Nicole V. Anayannis, Stephanie Cabarcas-Petroski, Laura Schramm and Patricio I. Meneses
Int. J. Mol. Sci. 2022, 23(18), 10967; https://doi.org/10.3390/ijms231810967 - 19 Sep 2022
Cited by 7 | Viewed by 2833
Abstract
High-risk human papillomaviruses (HPV) are important agents, responsible for a large percentage of the 745,000 cases of head and neck squamous cell carcinomas (HNSCC), which were identified worldwide in 2020. In addition to being virally induced, tobacco and heavy alcohol consumption are believed [...] Read more.
High-risk human papillomaviruses (HPV) are important agents, responsible for a large percentage of the 745,000 cases of head and neck squamous cell carcinomas (HNSCC), which were identified worldwide in 2020. In addition to being virally induced, tobacco and heavy alcohol consumption are believed to cause DNA damage contributing to the high number of HNSCC cases. Gene expression and DNA methylation differ between HNSCC based on HPV status. We used publicly available gene expression and DNA methylation profiles from the Cancer Genome Atlas and compared HPV positive and HPV negative HNSCC groups. We used differential gene expression analysis, differential methylation analysis, and a combination of these two analyses to identify the differences. Differential expression analysis identified 1854 differentially expressed genes, including PCNA, TNFRSF14, TRAF1, TRAF2, BCL2, and BIRC3. SYCP2 was identified as one of the top deregulated genes in the differential methylation analysis and in the combined differential expression and methylation analyses. Additionally, pathway and ontology analyses identified the extracellular matrix and receptor interaction pathway as the most altered between HPV negative and HPV positive HNSCC groups. Combining gene expression and DNA methylation can help in elucidating the genes involved in HPV positive HNSCC tumorigenesis, such as SYCP2 and TAF7L. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Control of Disease Occurrence)
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Review

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19 pages, 885 KiB  
Review
Viral and Non-Viral Systems to Deliver Gene Therapeutics to Clinical Targets
by Maryam Taghdiri and Claudio Mussolino
Int. J. Mol. Sci. 2024, 25(13), 7333; https://doi.org/10.3390/ijms25137333 - 4 Jul 2024
Cited by 21 | Viewed by 7516
Abstract
Clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has revolutionized the field of gene therapy as it has enabled precise genome editing with unprecedented accuracy and efficiency, paving the way for clinical applications to treat otherwise incurable genetic disorders. Typically, [...] Read more.
Clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has revolutionized the field of gene therapy as it has enabled precise genome editing with unprecedented accuracy and efficiency, paving the way for clinical applications to treat otherwise incurable genetic disorders. Typically, precise genome editing requires the delivery of multiple components to the target cells that, depending on the editing platform used, may include messenger RNA (mRNA), protein complexes, and DNA fragments. For clinical purposes, these have to be efficiently delivered into transplantable cells, such as primary T lymphocytes or hematopoietic stem and progenitor cells that are typically sensitive to exogenous substances. This challenge has limited the broad applicability of precise gene therapy applications to those strategies for which efficient delivery methods are available. Electroporation-based methodologies have been generally applied for gene editing applications, but procedure-associated toxicity has represented a major burden. With the advent of novel and less disruptive methodologies to deliver genetic cargo to transplantable cells, it is now possible to safely and efficiently deliver multiple components for precise genome editing, thus expanding the applicability of these strategies. In this review, we describe the different delivery systems available for genome editing components, including viral and non-viral systems, highlighting their advantages, limitations, and recent clinical applications. Recent improvements to these delivery methods to achieve cell specificity represent a critical development that may enable in vivo targeting in the future and will certainly play a pivotal role in the gene therapy field. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Control of Disease Occurrence)
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32 pages, 1763 KiB  
Review
The Epigenetics of Migraine
by Farzin Zobdeh, Ivan I. Eremenko, Mikail A. Akan, Vadim V. Tarasov, Vladimir N. Chubarev, Helgi B. Schiöth and Jessica Mwinyi
Int. J. Mol. Sci. 2023, 24(11), 9127; https://doi.org/10.3390/ijms24119127 - 23 May 2023
Cited by 13 | Viewed by 4275
Abstract
Migraine is a complex neurological disorder and a major cause of disability. A wide range of different drug classes such as triptans, antidepressants, anticonvulsants, analgesics, and beta-blockers are used in acute and preventive migraine therapy. Despite a considerable progress in the development of [...] Read more.
Migraine is a complex neurological disorder and a major cause of disability. A wide range of different drug classes such as triptans, antidepressants, anticonvulsants, analgesics, and beta-blockers are used in acute and preventive migraine therapy. Despite a considerable progress in the development of novel and targeted therapeutic interventions during recent years, e.g., drugs that inhibit the calcitonin gene-related peptide (CGRP) pathway, therapy success rates are still unsatisfactory. The diversity of drug classes used in migraine therapy partly reflects the limited perception of migraine pathophysiology. Genetics seems to explain only to a minor extent the susceptibility and pathophysiological aspects of migraine. While the role of genetics in migraine has been extensively studied in the past, the interest in studying the role of gene regulatory mechanisms in migraine pathophysiology is recently evolving. A better understanding of the causes and consequences of migraine-associated epigenetic changes could help to better understand migraine risk, pathogenesis, development, course, diagnosis, and prognosis. Additionally, it could be a promising avenue to discover new therapeutic targets for migraine treatment and monitoring. In this review, we summarize the state of the art regarding epigenetic findings in relation to migraine pathogenesis and potential therapeutic targets, with a focus on DNA methylation, histone acetylation, and microRNA-dependent regulation. Several genes and their methylation patterns such as CALCA (migraine symptoms and age of migraine onset), RAMP1, NPTX2, and SH2D5 (migraine chronification) and microRNA molecules such as miR-34a-5p and miR-382-5p (treatment response) seem especially worthy of further study regarding their role in migraine pathogenesis, course, and therapy. Additionally, changes in genes including COMT, GIT2, ZNF234, and SOCS1 have been linked to migraine progression to medication overuse headache (MOH), and several microRNA molecules such as let-7a-5p, let-7b-5p, let-7f-5p, miR-155, miR-126, let-7g, hsa-miR-34a-5p, hsa-miR-375, miR-181a, let-7b, miR-22, and miR-155-5p have been implicated with migraine pathophysiology. Epigenetic changes could be a potential tool for a better understanding of migraine pathophysiology and the identification of new therapeutic possibilities. However, further studies with larger sample sizes are needed to verify these early findings and to be able to establish epigenetic targets as disease predictors or therapeutic targets. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Control of Disease Occurrence)
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